Structure of PDB 5xd1 Chain A Binding Site BS01

Receptor Information
>5xd1 Chain A (length=292) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHTVRAAGAVLWRDPATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAR
EIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDK
LVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYK
GDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQEL
DQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIE
WWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK
Ligand information
Ligand ID5FA
InChIInChI=1S/C10H18N5O19P5/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(30-10)1-29-36(21,22)32-38(25,26)34-39(27,28)33-37(23,24)31-35(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H,25,26)(H,27,28)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyWYJWVZZCMBUPSP-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H18 N5 O19 P5
NameADENOSINE-5'-PENTAPHOSPHATE
ChEMBL
DrugBankDB02738
ZINCZINC000058632138
PDB chain5xd1 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xd1 Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1
Resolution1.6 Å
Binding residue
(original residue number in PDB)		R55 Y58 K65 G66 K67 Y101 K108 E127 Y145
Binding residue
(residue number reindexed from 1)		R25 Y28 K35 G36 K37 Y71 K78 E97 Y115
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) T23 A29
Catalytic site (residue number reindexed from 1) T3 A9
Enzyme Commision number 3.6.1.58: 8-oxo-dGDP phosphatase.
3.6.1.61: diadenosine hexaphosphate hydrolase (ATP-forming).
3.6.1.69: 8-oxo-(d)GTP phosphatase.
Gene Ontology
Molecular Function
GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0044715 8-oxo-dGDP phosphatase activity
GO:0044716 8-oxo-GDP phosphatase activity
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5xd1, PDBe:5xd1, PDBj:5xd1
PDBsum5xd1
PubMed28705712
UniProtA0QUZ2|MUTT1_MYCS2 8-oxo-(d)GTP phosphatase (Gene Name=mutT1)

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